Aligning two edge loops
The answer is easy. Blender has no idea which edge loops you consider to be connected. In Blender, connected means there have to be edges between the verts. Your top and bottom edgelines are not connected and logical, implied connections do not count. The local symmetry of the topology of your eyes isn't picked up by the selection tool.

You can use Box-, Lasso- or Circle Select or you can add to the selection using Loop Select more than once, SHIFTALTRMB. If you needed a certain selection a lot, you could even assign the verts to a vertex group and select them that way. But Loop Select will not bridge gaps. Your topology is not to blame.